Was putting together an order of the dragon cavalier for a PFS game and I wanted to see what I could do with the aid allies ability. I went online for ideas and found all the rules discussions talking about what does and doesn't stack with it. This was surprising as this was not at all the reading my home group has of the ability. This is our case:
Helpful (Halfling): "Whenever you successfully perform an aid another action, you grant your ally a +4 bonus instead of the normal +2."
Helpful: "When using the aid another action, you grant your ally a +3 bonus instead of a +2 bonus."
Aid Allies (Shadow lodge trait): "When using the aid another action, you give your ally a +3 bonus instead of a +2 bonus."
Improved Aid (Ex)(Pathfinder Chronicler power): "Pathfinder chroniclers frequently serve as the companions of great heroes, standing by their sides and recording their deeds, but often lending a crucial helping hand. Starting at 3rd level, a Pathfinder chronicler using the aid another action grants a +4 bonus, rather than the normal +2."
Fools for Friends (Second Darkness): "Whenever you take the aid another action to help an ally, or whenever an ally aids you in this manner, a successful check grants an additional +1 trait bonus to the check for which aid was being rendered. Additionally, as long as one of your friends is within 30 feet, you gain a +1 trait bonus on all saving throws against charm and compulsion effects."
Now the Aid Allies ability
Aid Allies: "At 2nd level, whenever an order of the dragon cavalier uses the aid another action to assist one of his allies, the ally receives a +3 bonus to his armor class, attack roll, saving throw, or skill check. At 8th level, and every six levels thereafter, this bonus increases by an additional +1."
Aid Allies does not seem to read as a modification to the aid another action but as a separate ability. In every case where the new bonus is meant to replace the +2 granted by the standard aid another action, it is specifically called out as granting a +3 or +4 instead of the normal +2. In the case where a +1 bonus is granted in Fools for Friends, it is specifically stated to grant a +1 trait bonus.
Aid Allies does none of these things. It does not say it replaces the normal +2 bonus, and it does not say that it grants a +1 bonus. It does not even say the Aid Allies has to go to the same ability you're aiding with the aid another action. To back this up, Aid Allies specifically states that you may grant a +3 bonus to a saving throw, which is not stated in the normal aid another action, it's barely implied as an afterthought text. It looks to us like a separate ability that triggers off of the aid another action.
For example, a cavalier uses the aid another action to give an ally a +2 bonus to an attack roll, he then uses the aid allies power to give that same ally a +3 bonus to his ac.
Thoughts?
I've had the same question. I think the "majority" were saying how you used it in your example. It's a separate bonus that goes when you aid another. But it wasn't a very big majority, or a big responding base. There's so many of these little questions that will probably never get address so you just have to make do. Best bet is talk to GM about it.